Scripts for image analysis using ImageJ(java), SQL, R, and LaTex.
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Updated
Mar 3, 2017 - R
Scripts for image analysis using ImageJ(java), SQL, R, and LaTex.
HPO archive of the ontology and annotations
Fully convolutional neural net for segmenting wing vein architecture from images of the wing of Drosophila melanogaster. Additional tools for computing persistent homology on the resulting segmented images.
Project to generate phenotype opposite_of relationships and investigate the effect on ontology-based algorithms
an R package for predicting plant biomass accumulation based on image-derived parameters
🐟 Zebrafish Phenotype Ontology: Build Tools (OBSOLETE)
HPO web browser created with Vaadin
Rosette Detection with SVM
The version of PAT64 that Jiwan used to analyse data for the W8 experiment
Code accompanying our CIKM paper: "copa: constrained parafac2 for sparse & large datasets"
Hybrid NMF to integrate genomic data and phenotype data for better patient subtyping. Paper in Bioinformatics.
Bayesian ontology querying from Bauer et al.
Code to generate ontology annotated objects (e.g. HPO annotated patients)
3-Demeter Capture is a tool for building 3-D point clouds from images
An imaging library to detect and track future position of ears on maize plants
Humbug is a multi-platform barcode generator which can be used alongside our Germinate Scan application to generate sheets of user-defined barcodes to aid in the recording of data in the field or glasshouse.
A pipeline to process multiframe tifs exported from ImagingWin .pim files
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